6-125881163-T-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181782.5(NCOA7):c.533T>A(p.Val178Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
NCOA7
NM_181782.5 missense
NM_181782.5 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 3.27
Genes affected
NCOA7 (HGNC:21081): (nuclear receptor coactivator 7) Enables nuclear receptor binding activity and nuclear receptor coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2349956).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NCOA7 | NM_181782.5 | c.533T>A | p.Val178Asp | missense_variant | 6/16 | ENST00000392477.7 | NP_861447.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NCOA7 | ENST00000392477.7 | c.533T>A | p.Val178Asp | missense_variant | 6/16 | 1 | NM_181782.5 | ENSP00000376269 | ||
NCOA7 | ENST00000368357.7 | c.533T>A | p.Val178Asp | missense_variant | 7/17 | 1 | ENSP00000357341 | |||
NCOA7 | ENST00000229634.13 | c.221T>A | p.Val74Asp | missense_variant | 5/15 | 2 | ENSP00000229634 | |||
NCOA7 | ENST00000417494.5 | c.533T>A | p.Val178Asp | missense_variant | 6/6 | 2 | ENSP00000406363 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
1
AN:
152196
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461680Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727136
GnomAD4 exome
AF:
AC:
4
AN:
1461680
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
727136
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74350
GnomAD4 genome
AF:
AC:
1
AN:
152196
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74350
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2024 | The c.533T>A (p.V178D) alteration is located in exon 8 (coding exon 5) of the NCOA7 gene. This alteration results from a T to A substitution at nucleotide position 533, causing the valine (V) at amino acid position 178 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N;D;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;D;T
Polyphen
P;P;.;.
Vest4
MutPred
Loss of glycosylation at S181 (P = 0.1098);Loss of glycosylation at S181 (P = 0.1098);Loss of glycosylation at S181 (P = 0.1098);.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at